Currently db_ucsc and db_ensembl are available for connections.

db_ucsc(
  dbname,
  host = "genome-mysql.cse.ucsc.edu",
  user = "genomep",
  password = "password",
  port = 3306,
  ...
)

db_ensembl(
  dbname,
  host = "ensembldb.ensembl.org",
  user = "anonymous",
  password = "",
  port = 3306,
  ...
)

Arguments

dbname

name of database

host

hostname

user

username

password

password

port

MySQL connection port

...

params for connection

See also

Examples

if (FALSE) { if(require(RMySQL)) { ucsc <- db_ucsc('hg38') # fetch the `refGene` tbl tbl(ucsc, "refGene") # the `chromInfo` tbls have size information tbl(ucsc, "chromInfo") } } if (FALSE) { if(require(RMySQL)) { # squirrel genome ensembl <- db_ensembl('spermophilus_tridecemlineatus_core_67_2') tbl(ensembl, "gene") } }